Contacts of the helix formed by residues 214 - 224 (chain D) in PDB entry 2Q41
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D LYS* 3.1 46.7 + - - +
211D GLU* 3.3 24.0 + - - +
213D PHE* 1.3 82.2 - - - +
215D LYS* 1.3 65.8 + - - +
216D PRO* 3.4 12.2 - - + +
217D PHE* 3.2 13.9 + - - +
218D PHE* 3.3 16.0 + - - -
251D ASN* 4.2 5.6 - - - +
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Residues in contact with LYS 215 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D GLU* 1.3 69.9 - - - +
216D PRO* 1.3 73.8 - - + +
218D PHE* 3.3 9.0 + - - +
219D GLN* 3.1 24.1 + - - +
251D ASN* 3.5 37.0 - - + +
254D GLU* 2.8 41.1 + - - -
255D ILE* 4.5 19.4 - - + +
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Residues in contact with PRO 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LYS* 5.9 6.8 - - - +
211D GLU* 5.5 5.8 - - + +
214D GLU* 3.4 15.3 - - + +
215D LYS* 1.3 94.7 - - + +
217D PHE* 1.3 55.9 - - - +
219D GLN* 3.4 7.2 + - + +
220D SER* 3.1 24.9 + - - -
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Residues in contact with PHE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 3.8 20.2 - - + -
184D VAL* 4.6 19.5 - - + -
187D LEU* 3.3 24.0 - - + -
198D VAL* 5.2 0.4 - - + -
200D VAL* 3.5 26.5 - - + -
211D GLU* 3.3 25.4 + - + +
212D LEU* 3.4 51.4 - - + -
214D GLU 3.2 4.9 + - - +
215D LYS 3.2 0.6 - - - -
216D PRO* 1.3 76.8 - - - +
218D PHE* 1.3 67.9 + + - +
219D GLN 2.9 10.5 + - - -
220D SER* 3.0 8.0 + - - -
221D VAL* 2.9 45.4 + - + +
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Residues in contact with PHE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LEU 3.7 17.5 - - - -
213D PHE* 3.0 30.7 - + - -
214D GLU 3.3 19.0 + - - -
215D LYS 3.3 7.8 + - - +
217D PHE* 1.3 83.8 - + - +
219D GLN* 1.3 56.6 + - - +
221D VAL* 3.9 5.8 - - + -
222D ALA* 3.5 10.2 + - - +
231D VAL* 4.9 7.4 - - + -
233D THR* 4.0 27.1 - - + -
248D ILE* 4.3 11.4 - - + -
251D ASN* 4.4 10.3 - - + -
252D CYS* 3.7 33.4 - - - -
255D ILE* 2.9 32.8 - - + +
256D PHE* 3.7 22.5 - + + -
278D MSE 5.9 0.4 - - + -
280D CYS* 6.2 0.2 - - - -
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Residues in contact with GLN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LYS 3.1 15.5 + - - +
216D PRO* 3.4 8.7 - - + +
217D PHE 2.9 0.6 - - - -
218D PHE* 1.3 77.9 - - - +
220D SER* 1.3 65.4 + - - +
221D VAL 3.0 1.6 - - - -
222D ALA* 3.0 12.1 + - - +
223D ARG* 3.0 28.1 + - - +
255D ILE* 3.5 26.2 - - + +
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Residues in contact with SER 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D VAL* 5.0 3.2 + - - -
187D LEU* 3.3 25.0 + - - +
188D LYS* 3.5 29.2 + - - +
216D PRO 3.1 10.1 + - - -
217D PHE* 3.0 13.8 + - - -
219D GLN* 1.3 80.1 - - - +
221D VAL* 1.3 57.7 + - - +
223D ARG* 3.6 10.4 + - - +
224D ALA* 3.1 29.1 + - - +
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LEU* 3.9 9.6 - - + -
198D VAL* 4.1 14.4 - - + -
217D PHE* 2.9 51.2 + - + +
218D PHE* 4.2 8.5 - - + +
220D SER* 1.3 76.5 - - - +
222D ALA* 1.3 58.9 + - - +
223D ARG 3.2 0.4 - - - -
224D ALA* 3.9 4.7 - - - -
225D LEU* 3.0 46.8 + - + +
231D VAL* 3.3 42.4 - - + -
256D PHE* 4.5 0.4 - - + -
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D PHE 3.5 14.5 + - - +
219D GLN* 3.0 18.7 + - - +
221D VAL* 1.3 81.2 - - - +
223D ARG* 1.3 59.4 + - - +
225D LEU 3.8 8.5 - - - +
255D ILE* 3.7 21.3 - - + +
256D PHE* 4.3 8.3 - - + -
282D THR* 3.9 21.3 - - + +
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Residues in contact with ARG 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LEU 3.6 9.5 + - - -
188D LYS* 3.0 24.5 + - - +
190D ALA 2.6 22.0 + - - -
191D ALA 3.1 6.6 + - - -
192D GLU* 3.0 67.2 - - + +
193D GLY 3.0 17.8 + - - -
219D GLN* 3.0 18.4 + - - +
220D SER* 4.0 8.5 + - - +
222D ALA* 1.3 75.4 - - - +
224D ALA* 1.3 70.9 + - - +
225D LEU 3.0 8.9 - - - +
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LEU* 3.5 26.5 - - + +
190D ALA* 5.8 0.9 - - + -
191D ALA 4.2 16.4 - - - +
193D GLY 3.8 0.7 - - - -
194D SER 3.4 6.4 + - - -
195D TYR* 3.1 37.7 + - + +
198D VAL* 5.2 3.8 - - + -
220D SER 3.1 16.8 + - - +
221D VAL* 4.0 3.6 - - - +
223D ARG* 1.3 84.4 - - - +
225D LEU* 1.3 60.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il